Last year's Cheltenham Gold Cup winner will be re-routed to the John Durkan Memorial Chase at Punchestown on December 10.
"Sadly he's not running because the ground is soft, heavy in places and there's a bit more rain due," said Harrington.
"It's just the ground. I've been a bit worried all week. I didn't mind soft, genuine soft ground, but when they start putting heavy into Haydock, it gets very heavy.
"Plan B will be the John Durkan and then we'll take it from there."
The decision means Sizing John will not be attempting the £1million bonus offered by the Jockey Club to a horse that wins the Betfair Chase, the 32Red King George VI Chase and Timico Cheltenham Gold Cup in the same season.
The seven-year-old, owned by the late Ann and Alan Potts, was last seen winning the Punchestown Gold Cup in April.
In contrast, Traffic Fluide will take his chance at Haydock rather than tackle an alternative engagement at Ascot.
Gary Moore entered the seven-year-old in the Grade Two Christy 1965 Chase along with the Grade One feature on Merseyside, after he finished fourth in the Old Roan Chase at Aintree on his return.
However, Traffic Fluide will take the top-level option and step up to three miles for the first time, with Moore expecting testing ground to suit.
He said: "He goes to Haydock - I would say the opposition is more of a worry than the trip. It's a tough race. It will be the first time he's really got his ground, he didn't really get it last year.
"He likes it testing and it might just help level it up a bit."
Speaking before news of Sizing John's absence, Moore added: "It's almost like a Gold Cup, but we're keen to give it a go and so is the owner, so we'll take our chance."